Genome wide association study for salmon lice (Lepeophtheirus salmonis) resistance in Atlantic salmon (Salmo salar)

My objective was to detect single nucleotide polymorphism (SNP) associations with salmon lice resistance in an aquacultural population of Saint John River Atlantic salmon. In 2011 and 2012 I challenged recent smolts with copepodids from 42 and 47 families respectively. Fish were euthanized once the lice reached the chalimus stages and lice count, sex, tank and weight were recorded. I used a multiple trait model to estimate breeding values for parents of challenged fish using fresh water weights collected on the parent generation and the salt water weights and lice counts collected on the challenged fish. Using 299 individuals that had deregressed estimated breeding values and had been genotyped for 3638 SNPs, I detected 70 SNP associations using a forward regression. I was able to detect SNP associations with salmon lice resistance which, with further research could lead to genomic selection for this economically important trait.